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- PDB-6mkw: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mkw | |||||||||||||||
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Title | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with histidine | |||||||||||||||
![]() | Lysine/arginine/ornithine transport protein | |||||||||||||||
![]() | PROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex | |||||||||||||||
Function / homology | ![]() amino acid transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Romero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein. Authors: Vergara, R. / Romero-Romero, S. / Velazquez-Lopez, I. / Espinoza-Perez, G. / Rodriguez-Hernandez, A. / Pulido, N.O. / Sosa-Peinado, A. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
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Full document | ![]() | 442 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mkuC ![]() 6mkxC ![]() 6ml0C ![]() 6ml9C ![]() 6mlaC ![]() 6mldC ![]() 6mleC ![]() 6mlgC ![]() 6mliC ![]() 6mljC ![]() 6mlnC ![]() 6mloC ![]() 6mlpC ![]() 6mlvC ![]() 1lagS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 25943.225 Da / Num. of mol.: 1 / Mutation: D11A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 14028s / SGSC 2262 / Gene: argT, STM14_2901 / Plasmid: pET12b / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-HIS / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate 30% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 10, 2018 / Details: Osmic VariMax Cu-HF |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 11213 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1055 / CC1/2: 0.885 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LAG Resolution: 2.32→35.148 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→35.148 Å
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Refine LS restraints |
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LS refinement shell |
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